Davide It kinda depends on what you want. The integrated system isn't bad, it works just fine for most purposes. It just offers fewer options overall, so if you need more advanced automation, then there's no way around Flow (or of course, if you're so inclined, you can always write your own Python/PHP/Node.js scripts to automate your banking).
Personally I use Flow for some automatization, because I have an inbox sub-account where I want all incoming payments to get automatically sorted. That is something that the bunq app itself cannot do, it can only sort payments that it already knows (for example if you get a salary payment every month from the same employer).
There are also some other things that Flow can do that the bunq app cannot do on its own: for example sending a transaction over a certain amount every month, so that the balance on an account is exactly 0 or any other amount you choose. For budgeting with multiple accounts, this can come in quite handy, if you want to make sure that you always have a certain amount available every month and you want to save any money that gets left over.
But if you don't care too much about these subtleties, then the integrated payment sorter does a fine job. And it's always nice to have less third-parties to worry about.